RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures |
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| Authors: | Mariusz Popenda Marta Szachniuk Marek Blazewicz Szymon Wasik Edmund K Burke Jacek Blazewicz Ryszard W Adamiak |
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| Institution: | (1) Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland;(2) Institute of Computing Science, Poznan University of Technology, Poznan, Poland;(3) Poznan Supercomputing and Networking Centre, Poznan, Poland;(4) Automated Scheduling, Optimisation and Planning Group, School of Computer Science, University of Nottingham, Nottingham, UK |
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| Abstract: | Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance
of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their
new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB,
NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible
database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon
the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version
of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities.
An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their
multi-parameter conformational analysis and visualization. |
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